Agencies seeking to build a water tunnel beneath the crucial Sacramento-San Joaquin River Delta have unclear goals and have not considered the effect on endangered fish species, a report says.

A proposal to build a large water tunnel under the Sacramento-San Joaquin River Delta is incomplete, confused and plagued by a number of scientific gaps despite years of study, according to a National Research Council report.

The document bolsters criticisms that the agencies overseeing the project are not seriously evaluating alternatives and are instead pursuing a preordained outcome without examining the effects.

"The lack of an appropriate structure creates the impression that the entire effort is little more than a post-hoc rationalization of a previously selected group of facilities," write the authors, an independent panel of scientists and other experts.

The investigators did not find the shortcomings fatal, however, saying that the scientific work done so far has been good. "There is a solid beginning here," said panel Chairman Henry Vaux Jr., associate vice president emeritus of UC Berkeley. "This plan can be made more complete and stronger."

The review faults the draft Bay Delta Conservation Plan released late last year on a variety of counts, including unclear goals and the lack of an analysis of the proposal's effects on the delta's endangered fish species. The report notes that the plan gives the size of the proposed tunnel, but never says how much water will be diverted through it, making it "nearly impossible to evaluate."

Officials of the federal agencies that requested the critique welcomed the findings. "We will use it as a guide," Deputy Interior Secretary David Hayes said. He added that the plan remains a work in progress and will include alternatives as part of required environmental reviews.

"We are not prejudging what the answer will be," he said.

The conservation plan is the latest attempt to save the delta and its native fish while continuing to use the estuary as a giant faucet for much of the state. The proposal calls for extensive habitat restoration and construction of water conveyance facilities — probably a subterranean tunnel — to reduce the water withdrawals from the southern delta, which are harming the imperiled delta smelt and migrating salmon.

A group of state and federal agencies, water users and conservationists are working, not always harmoniously, on the proposal, which if adopted would grant the delta's big state and federal water operations a 50-year environmental permit.

Major San Joaquin Valley irrigation districts have complained that the project may not deliver all the water they want, while environmentalists say the proposal focuses too much on a large-capacity tunnel without adequately investigating its ecological effects or examining alternatives.

"There is a lot of work to be done and that work hasn't been done from our point of view," said Jon Rosenfield, a conservation biologist with the Bay Institute. "I'm hopeful this will be a splash of cold water."